Surprisingly, slop (within reason) in the pedal mechanism has little impact on how well it shifts the transmission. If the clutch drags even the slightest bit, 1st, 2nd and neutral can be super hard to sort out when the bike is not rolling so investigating that is in order, and I'll second the notion of the oil having a potentially big impact on the clutch. The angle of the bellcranks, rod and foot lever do make a difference. You have the pivot on the front crank arm arranged so that there is a limit on the angle it can work through before it binds so make sure that it doesn't if you haven't already. The whole mechanism is more bendy and deflects a lot more in actual use than you might expect working it by hand so make sure there is an excess of available motion. As long as there is no binding, I think the way you have the front pivot is fine. There can also be binding at the pedal pivot as there are side loads in actual operation that you don't tend to notice in hand operation.
Also keep in mind that your foot and ankle orientation, and the angle your ankle has to rotate has a big impact on how hard or easy things seem - not to mention it is easier to push down with your foot than it is to lift up with your toe.
It is challenging to explain the impact of orienting the angles between the crank arms, pedal lever, and rod without some diagrams, but using your photo as a base I'll give it a shot. Starting with 900 between the elements is always a good idea as J-Rod says, but because the amount of rotation of the cranks is large compared to their lengths, more info is useful.
First though, go back and get the original shifter pedal and compare its length to the new one. If it is longer, your trans will be noticeably harder to shift with the new shorter pedal assuming the two crank arms on the new mechanism are the same length. You can restore the original leverage by changing the length of the crank arms. If your original pedal is 20% longer than your new one, you need the driven crank arm (the one attached to the shift shaft) to be 20% longer than the drive arm. If this adjustment is not a complete solution, you still have some big tuning capacity in the crank arm angles.
Look at your pic and observe the angle between the drive crank arm and the connecting rod. The angle is much greater than 900. Consider the effort required to move the rod in each direction. When you lift up on the pedal, the angle will increase. As it does, the mechanical advantage over the rod will increase, so pedal effort needed will decrease the farther it rotates. This makes the bike easier to upshift force-wise, but you pay for this with longer travel distance of the pedal. When you down shift, the angle becomes more acute as it comes up to 900, and the force becomes greater, and the pedal distance traveled becomes shorter.
This principle works in reverse at the other end of the push/pull rod. In your pic, the angle is less than 900 and as the rod pushes the crank, the angle becomes more acute and the force required to rotate the crank increases. As you pull on the rod, the force needed decreases until 900 is reached, and then the force required will increase as the angle gets farther away from perpendicular.
The effect of the angle between the rod and crank arm is opposite depending on if it is the drive arm or driven arm. A bit hard to tell from your pic due to lens distortion, but it looks like the two crank arm are pretty close to parallel. This has the effect of canceling each other out. When the drive arm has greater mechanical advantage when pushing the rod due to angle, (or less when pulling) the driven arm has less advantage when being pushed (or more when pulling) and the force on the shift shaft is the same as the pedal shaft - it's a wash.
This only works for fairly small deviations from 900. Consider the crank on the shift shaft. If you rotated it counterclockwise a bit, it would have a 900 angle with the rod. Consider pushing on the rod. At 900, 10 lbs of force will displace the crank against the spring a certain distance. If you re-index the crank clockwise, the force required to achieve the same displacement against the same spring pressure will go up. As the rotation goes up, the force needed goes up very rapidly. In fact, imagine having to rotate the crank a full 900 - as the crank arm comes up to 900, the force needed to rotate it goes to infinity. So fairly small deviations from the 900 relationship between the various parts can have a very noticeable effect.
So work on the easy and obvious stuff first. Check the mechanism for binding, and fix any pedal length issue. Try some new oil - you probably want to change oil on a new motor anyway. If your still not happy, you can make a big difference by fooling around with the crank angles.